Modelling responses to a smallpox epidemic taking into account uncertainty

Modelling of optimal vaccination strategies in response to a bioterrorism associated smallpox outbreak

The reemergence of smallpox as a bioterrorism attack is now an increasing and legitimate concern. Advances in synthetic biology have now made it possible for the virus to be synthesized in a laboratory, with methods publicly available. Smallpox introduction into a susceptible population, with increased immunosuppression and an aging population, raises questions of how vaccination should be used in an epidemic situation when supply may be limited. We constructed three modified susceptible-latent-infectious-recovered (SEIR) models to simulate targeted, ring and mass vaccination in response to a smallpox outbreak in Sydney, Australia. We used age-specific distributions of susceptibility, infectivity, contact rates, and tested outputs under different assumptions. The number of doses needed of second- and third-generation vaccines are estimated, along with the total number of deaths at the end of the epidemic. We found a faster response is the key and ring vaccination of traced contacts is the most effective strategy and requires a smaller number of doses. However if public health authorities are unable to trace a high proportion of contacts, mass vaccination with at least 125,000 doses delivered per day is required. This study informs a better preparedness and response planning for vaccination in a case of a smallpox outbreak in a setting such as Sydney.

The Effect of Climate Change and the Snail-Schistosome Cycle in Transmission and Bio-Control of Schistosomiasis in Sub-Saharan Africa

In the next century, global warming, due to changes in climatic factors, is expected to have an enormous influence on the interactions between pathogens and their hosts. Over the years, the rate at which vector-borne diseases and their transmission dynamics modify and develop has been shown to be highly dependent to a certain extent on changes in temperature and geographical distribution. Schistosomiasis has been recognized as a tropical and neglected vector-borne disease whose rate of infection has been predicted to be elevated worldwide, especially in sub-Saharan Africa; the region currently with the highest proportion of people at risk, due to changes in climate. This review not only suggests the need to develop an efficient and effective model that will predict Schistosoma spp. population dynamics but seeks to evaluate the effectiveness of several current control strategies. The design of a framework model to predict and accommodate the future incidence of schistosomiasis in human population dynamics in sub-Saharan Africa is proposed. The impact of climate change on schistosomiasis transmission as well as the distribution of several freshwater snails responsible for the transmission of Schistosoma parasites in the region is also reviewed. Lastly, this article advocates for modelling several control mechanisms for schistosomiasis in sub-Saharan Africa so as to tackle the re-infection of the disease, even after treating infected people with praziquantel, the first-line treatment drug for schistosomiasis.

How Valid Are Assumptions About Re-emerging Smallpox? A Systematic Review of Parameters Used in Smallpox Mathematical Models

Background

Globally eradicated in 1980, smallpox is listed as a category A bioterrorism agent. If smallpox were to re-emerge, it may be due to an act of bioterrorism or a laboratory accident, and the impact is likely to be severe. Preparedness against smallpox is subject to more uncertainty than other infectious diseases because it is eradicated, there is uncertainty about population immunity, and the current global health workforce has no practical experience or living memory of smallpox. In the event of re-emergence of smallpox, mathematical modeling plays a crucial role in improving the evidence base to inform preparedness, mitigation, and response activities. However, the predictions of mathematical models about outbreak magnitude and impact depend critically on the assumptions and disease parameters used. We aimed to identify modeling studies that would be applicable to re-emerging smallpox and to evaluate consistency and the certainty of the evidence published about the key parameters used.

Methods

We conducted a systematic review using PRISMA criteria, of assumptions used in modeling studies on duration of latent, prodromal, and infectious period, as well as the choice of the basic reproduction number (R0) for re-emerging smallpox. We performed a literature search using PubMED, Scopus, Web of Science, and EMBASE and included peer-reviewed articles that focused on smallpox models, stated at least three of the aforementioned parameters and published in English.

Findings

A total of 42 studies were selected for inclusion. There was general agreement on the duration of latent and prodromal periods, being 11-12 d (88%) and 3 d (59%), respectively. The duration of the infectious period varied from 4 to 20 d. Most models assumed 16 d (19%), 12 d (16.7%), and 8.6 d (12%) of infectiousness. In 25/34 studies, R0 ranged between 3 and 5, generally lower than the R0 calculated from past outbreaks.

Discussion

Models of smallpox re-emergence also tend to use the same limited available historical data sources but assume a wide range of different estimates for key parameters. Models use very optimistic assumptions of decreased population immunity, despite high uncertainty about duration and magnitude of post-vaccination immunity. This review reveals a paradox. A substantial proportion of the modern population is unvaccinated, never exposed to boosting from wild-type smallpox, or immunocompromised; furthermore, vaccine-induced immunity wanes over time. Failure to consider these factors in a model will lead to underestimating the true impact of a re-emergent smallpox epidemic in the contemporary population.

Real-time predictive seasonal influenza model in Catalonia, Spain

Influenza surveillance is critical to monitoring the situation during epidemic seasons and predictive mathematic models may aid the early detection of epidemic patterns. The objective of this study was to design a real-time spatial predictive model of ILI (Influenza Like Illness) incidence rate in Catalonia using one- and two-week forecasts. The available data sources used to select explanatory variables to include in the model were the statutory reporting disease system and the sentinel surveillance system in Catalonia for influenza incidence rates, the official climate service in Catalonia for meteorological data, laboratory data and Google Flu Trend. Time series for every explanatory variable with data from the last 4 seasons (from 2010–2011 to 2013–2014) was created. A pilot test was conducted during the 2014–2015 season to select the explanatory variables to be included in the model and the type of model to be applied. During the 2015–2016 season a real-time model was applied weekly, obtaining the intensity level and predicted incidence rates with 95% confidence levels one and two weeks away for each health region. At the end of the season, the confidence interval success rate (CISR) and intensity level success rate (ILSR) were analysed. For the 2015–2016 season a CISR of 85.3% at one week and 87.1% at two weeks and an ILSR of 82.9% and 82% were observed, respectively. The model described is a useful tool although it is hard to evaluate due to uncertainty. The accuracy of prediction at one and two weeks was above 80% globally, but was lower during the peak epidemic period. In order to improve the predictive power, new explanatory variables should be included.

Influenza A virus in swine breeding herds: Combination of vaccination and biosecurity practices can reduce likelihood of endemic piglet reservoir

Recent modelling and empirical work on influenza A virus (IAV) suggests that piglets play an important role as an endemic reservoir. The objective of this study is to test intervention strategies aimed at reducing the incidence of IAV in piglets and ideally, preventing piglets from becoming exposed in the first place. These interventions include biosecurity measures, vaccination, and management options that swine producers may employ individually or jointly to control IAV in their herds. We have developed a stochastic Susceptible-Exposed-Infectious-Recovered-Vaccinated (SEIRV) model that reflects the spatial organization of a standard breeding herd and accounts for the different production classes of pigs therein. Notably, this model allows for loss of immunity for vaccinated and recovered animals, and for vaccinated animals to have different latency and infectious periods from unvaccinated animals as suggested by the literature. The interventions tested include: (1) varied timing of gilt introductions to the breeding herd, (2) gilt separation (no indirect transmission to or from the gilt development unit), (3) gilt vaccination upon arrival to the farm, (4) early weaning, and (5) vaccination strategies of sows with different timing (mass and pre-farrow) and efficacy (homologous vs. heterologous). We conducted a Latin Hypercube Sampling and Partial Rank Correlation Coefficient (LHS-PRCC) analysis combined with a random forest analysis to assess the relative importance of each epidemiological parameter in determining epidemic outcomes. In concert, mass vaccination, early weaning of piglets (removal 0-7days after birth), gilt separation, gilt vaccination, and longer periods between introductions of gilts (6 months) were the most effective at reducing prevalence. Endemic prevalence overall was reduced by 51% relative to the null case; endemic prevalence in piglets was reduced by 74%; and IAV was eliminated completely from the herd in 23% of all simulations. Importantly, elimination of IAV was most likely to occur within the first few days of an epidemic. The latency period, infectious period, duration of immunity, and transmission rate for piglets with maternal immunity had the highest correlation with three separate measures of IAV prevalence; therefore, these are parameters that warrant increased attention for obtaining empirical estimates. Our findings support other studies suggesting that piglets play a key role in maintaining IAV in breeding herds. We recommend biosecurity measures in combination with targeted homologous vaccination or vaccines that provide wider cross-protective immunity to prevent incursions of virus to the farm and subsequent establishment of an infected piglet reservoir.

Human mobility and the worldwide impact of intentional localized highly pathogenic virus release

The threat of bioterrorism and the possibility of accidental release have spawned a growth of interest in modeling the course of the release of a highly pathogenic agent. Studies focused on strategies to contain local outbreaks after their detection show that timely interventions with vaccination and contact tracing are able to halt transmission. However, such studies do not consider the effects of human mobility patterns. Using a large-scale structured metapopulation model to simulate the global spread of smallpox after an intentional release event, we show that index cases and potential outbreaks can occur in different continents even before the detection of the pathogen release. These results have two major implications: i) intentional release of a highly pathogenic agent within a country will have global effects; ii) the release event may trigger outbreaks in countries lacking the health infrastructure necessary for effective containment. The presented study provides data with potential uses in defining contingency plans at the National and International level.

Efficacy of tecovirimat (ST-246) in nonhuman primates infected with variola virus (Smallpox)

Naturally occurring smallpox has been eradicated but remains a considerable threat as a biowarfare/bioterrorist weapon (F. Fleck, Bull. World Health Organ. 81:917-918, 2003). While effective, the smallpox vaccine is currently not recommended for routine use in the general public due to safety concerns (http://www.bt.cdc.gov/agent/smallpox/vaccination). Safe and effective countermeasures, particularly those effective after exposure to smallpox, are needed. Currently, SIGA Technologies is developing the small-molecule oral drug, tecovirimat (previously known as ST-246), as a postexposure therapeutic treatment of orthopoxvirus disease, including smallpox. Tecovirimat has been shown to be efficacious in preventing lethal orthopoxviral disease in numerous animal models (G. Yang, D. C. Pevear, M. H. Davies, M. S. Collett, T. Bailey, et al., J. Virol. 79:13139-13149, 2005; D. C. Quenelle, R. M. Buller, S. Parker, K. A. Keith, D. E. Hruby, et al., Antimicrob. Agents Chemother., 51:689-695, 2007; E. Sbrana, R. Jordan, D. E. Hruby, R. I. Mateo, S. Y. Xiao, et al., Am. J. Trop. Med. Hyg. 76:768-773, 2007). Furthermore, in clinical trials thus far, the drug appears to be safe, with a good pharmacokinetic profile. In this study, the efficacy of tecovirimat was evaluated in both a prelesional and postlesional setting in nonhuman primates challenged intravenously with 1 × 10(8) PFU of Variola virus (VARV; the causative agent of smallpox), a model for smallpox disease in humans. Following challenge, 50% of placebo-treated controls succumbed to infection, while all tecovirimat-treated animals survived regardless of whether treatment was started at 2 or 4 days postinfection. In addition, tecovirimat treatment resulted in dramatic reductions in dermal lesion counts, oropharyngeal virus shedding, and viral DNA circulating in the blood. Although clinical disease was evident in tecovirimat-treated animals, it was generally very mild and appeared to resolve earlier than in placebo-treated controls that survived infection. Tecovirimat appears to be an effective smallpox therapeutic in nonhuman primates, suggesting that it is reasonably likely to provide therapeutic benefit in smallpox-infected humans.

Development of the small-molecule antiviral ST-246 as a smallpox therapeutic

Naturally occurring smallpox has been eradicated, yet it remains as one of the highest priority pathogens due to its potential as a biological weapon. The majority of the US population would be vulnerable in a smallpox outbreak. SIGA Technologies, Inc. has responded to the call of the US government to develop and supply to the Strategic National Stockpile a smallpox antiviral to be deployed in the event of a smallpox outbreak. ST-246(®) (tecovirimat) was initially identified via a high-throughput screen in 2002, and in the ensuing years, our drug-development activities have spanned in vitro analysis, preclinical safety, pharmacokinetics and efficacy testing (all according to the 'animal rule'). Additionally, SIGA has conducted Phase I and II clinical trials to evaluate the safety, tolerability and pharmacokinetics of ST-246, bringing us to our current late stage of clinical development. This article reviews the need for a smallpox therapeutic and our experience in developing ST-246, and provides perspective on the role of a smallpox antiviral during a smallpox public health emergency.

Smallpox as a Weapon for Bioterrorism

Smallpox, the only disease ever eradicated, is one of the six pathogens considered a serious threat for biological terrorism (Henderson et al., 1999; Mahy, 2003; Whitley, 2003). Smallpox has several attributes that make it a potential threat. It can be grown in large amounts. It spreads via the respiratory route. It has a 30% mortality rate. The potential for an attack using smallpox motivated President Bush to call for phased vaccination of a substantial number of American health care and public health workers (Grabenstein and Winkenwerder, 2003; Stevenson and Stolberg, 2002). Following September 11, 2001, the United States rebuilt its supplies of vaccine and Vaccinia Immune Globulin (VIG), expanded the network of laboratories capable of testing for variola virus, and engaged in a broad education campaign to help health care workers and the general public understand the disease (Centers for Disease Control and Prevention, 2003a). This chapter summarizes the scientific and theoretical bases for use of smallpox as a bioweapon and options for preparation for defense against it.

Extracting key information from historical data to quantify the transmission dynamics of smallpox

Background

Quantification of the transmission dynamics of smallpox is crucial for optimizing intervention strategies in the event of a bioterrorist attack. This article reviews basic methods and findings in mathematical and statistical studies of smallpox which estimate key transmission parameters from historical data.

Main findings

First, critically important aspects in extracting key information from historical data are briefly summarized. We mention different sources of heterogeneity and potential pitfalls in utilizing historical records. Second, we discuss how smallpox spreads in the absence of interventions and how the optimal timing of quarantine and isolation measures can be determined. Case studies demonstrate the following. (1) The upper confidence limit of the 99th percentile of the incubation period is 22.2 days, suggesting that quarantine should last 23 days. (2) The highest frequency (61.8%) of secondary transmissions occurs 3–5 days after onset of fever so that infected individuals should be isolated before the appearance of rash. (3) The U-shaped age-specific case fatality implies a vulnerability of infants and elderly among non-immune individuals. Estimates of the transmission potential are subsequently reviewed, followed by an assessment of vaccination effects and of the expected effectiveness of interventions.

Conclusion

Current debates on bio-terrorism preparedness indicate that public health decision making must account for the complex interplay and balance between vaccination strategies and other public health measures (e.g. case isolation and contact tracing) taking into account the frequency of adverse events to vaccination. In this review, we summarize what has already been clarified and point out needs to analyze previous smallpox outbreaks systematically.

Orthopoxvirus detection in environmental specimens during suspected bioterror attacks: inhibitory influences of common household products

After terrorists attacked the United States in 2001, the appearance of letters and other objects containing powdery substances with unknown potentials for biological threat focused attention on the speed, sensitivity, and reliability of diagnostic methods. This study summarizes the abilities and limitations of real-time PCR, electron microscopy (EM), and virus isolation when used to detect potential bioweapons. In particular, we investigated the inhibitory influences of different common household products present in environmental specimens on PCR yield, EM detection, and virus isolation. We used vaccinia virus as a model for orthopoxviruses by spiking it into specimens. In the second part of the study, we describe modifications of diagnostic methods to overcome inhibitory effects. A variety of PCR amplification enhancers, DNA extraction protocols, and applications of internal controls were evaluated to improve diagnostic simplicity, speed, and reliability. As a result, we strongly recommend using at least two different frontline techniques in parallel, e.g., EM and PCR. A positive result obtained by any one of these techniques should be followed by a biological method to confirm the putative diagnosis. Confirmatory methods include virus isolation followed by an agent-specific immunofluorescence assay to confirm the presence of replication-competent particles.

Characterization of UVC light sensitivity of vaccinia virus

Interest in airborne smallpox transmission has been renewed because of concerns regarding the potential use of smallpox virus as a biothreat agent. Air disinfection via upper-room 254-nm germicidal UV (UVC) light in public buildings may reduce the impact of primary agent releases, prevent secondary airborne transmission, and be effective prior to the time when public health authorities are aware of a smallpox outbreak. We characterized the susceptibility of vaccinia virus aerosols, as a surrogate for smallpox, to UVC light by using a benchtop, one-pass aerosol chamber. We evaluated virus susceptibility to UVC doses ranging from 0.1 to 3.2 J/m(2), three relative humidity (RH) levels (20%, 60%, and 80%), and suspensions of virus in either water or synthetic respiratory fluid. Dose-response plots show that vaccinia virus susceptibility increased with decreasing RH. These plots also show a significant nonlinear component and a poor fit when using a first-order decay model but show a reasonable fit when we assume that virus susceptibility follows a log-normal distribution. The overall effects of RH (P < 0.0001) and the suspending medium (P = 0.014) were statistically significant. When controlling for the suspending medium, the RH remained a significant factor (P < 0.0001) and the effect of the suspending medium was significant overall (P < 0.0001) after controlling for RH. Virus susceptibility did not appear to be a function of virus particle size. This work provides an essential scientific basis for the design of effective upper-room UVC installations for the prevention of airborne infection transmission of smallpox virus by characterizing the susceptibility of an important orthopoxvirus to UVC exposure.

Modelling outbreak control for pneumonic plague

Although pneumonic plague is listed by the Centers of Disease Control in the leading 'critical biological agents', very few studies exist on this subject. In this study, a mathematical compartment model was used to describe the geographical and temporal spread of an epidemic of pneumonic plague following its use as a biological weapon. Univariate and multivariate analyses were performed in order to assess the key parameters for the control of an outbreak in France. If interventions were taken 10 days after an attack, a reference scenario of 1000 index cases in Paris would lead to 2500 deaths. The results of the study indicate that the rapidity of onset of interventions has the largest effect on the final size of the epidemic, followed by wearing masks, treating contacts preventively and quarantine. Limiting inter-regional mixing does little to reduce casualties, although it does confine them to a single region.

Early disease management strategies in case of a smallpox outbreak

As a consequence of the threat of smallpox being potentially used as a means of bioterrorism, many countries have developed preparedness plans for smallpox in the past few years. This chapter summarizes some of the most important issues for the management of smallpox. Usually, the strategy for the management of clinical cases of poxviruses includes the early detection of cases, rapid laboratory diagnosis, an assessment of the risk of further spread and containment measures. For the early detection, different systems are being tested to identify suspected cases before a diagnosis is confirmed (e.g., syndromic surveillance). Also it is necessary to provide special training on the disease pattern, including differential diagnosis, to clinicians and practitioners. If a suspected case has been identified, rapid diagnostic tests are required. In addition to the national and international notifications based on given case definitions, certain measures are necessary to allow an initial risk assessment of the epidemic development. For a rapid risk assessment, the investigations should follow the algorithms of epidemiological outbreak investigation such as the tracing and identification of exposed contacts and the sources of infection. Further decisions have to be taken on the basis of a continuous risk assessment. Countermeasures can be divided into medical and non-medical ones. The choice of an adequate vaccination strategy as a medical countermeasure for the case of a re-emergence of smallpox very much depends on the epidemic scenario, and the general availability and quality of a vaccine. Logistic aspects of the vaccination strategies have to be considered in preparedness planning (e.g., resources necessary for the implementation of mass vaccinations), and also the prioritization of groups to be vaccinated. In addition non-medical measures to prevent the spread of infection, such as the isolation of cases and quarantining of exposed persons (e.g., contact persons of confirmed cases) have to be foreseen. The effectiveness of other measures like prohibition of mass gatherings or closure of institutions is often assessed in the light of historical events. However, they have to be considered within today’s ethical and societal context, taking into account, in particular, the increased number of people who are immunocompromised. Since our knowledge of how the virus would behave today is limited to extrapolations from historical data and is therefore imperfect, these measures are still under discussion. All relevant groups should be involved in exercises to assure the effective operation of the plan mainly regarding communication and cooperation.

Transmission patterns of smallpox: systematic review of natural outbreaks in Europe and North America since World War II

BACKGROUND

Because smallpox (variola major) may be used as a biological weapon, we reviewed outbreaks in post-World War II Europe and North America in order to understand smallpox transmission patterns.

METHODS

A systematic review was used to identify papers from the National Library of Medicine, Embase, Biosis, Cochrane Library, Defense Technical Information Center, WorldCat, and reference lists of included publications. Two authors reviewed selected papers for smallpox outbreaks.

RESULTS

51 relevant outbreaks were identified from 1,389 publications. The median for the effective first generation reproduction rate (initial R) was 2 (range 0-38). The majority outbreaks were small (less than 5 cases) and contained within one generation. Outbreaks with few hospitalized patients had low initial R values (median of 1) and were prolonged if not initially recognized (median of 3 generations); outbreaks with mostly hospitalized patients had higher initial R values (median 12) and were shorter (median of 3 generations). Index cases with an atypical presentation of smallpox were less likely to have been diagnosed with smallpox; outbreaks in which the index case was not correctly diagnosed were larger (median of 27.5 cases) and longer (median of 3 generations) compared to outbreaks in which the index case was correctly diagnosed (median of 3 cases and 1 generation).

CONCLUSION

Patterns of spread during Smallpox outbreaks varied with circumstances, but early detection and implementation of control measures is a most important influence on the magnitude of outbreaks. The majority of outbreaks studied in Europe and North America were controlled within a few generations if detected early.

Mass vaccination and surveillance/containment in the eradication of smallpox

The Smallpox Eradication Program, initiated by the WHO in 1966, was originally based on mass vaccination. The program emphasized surveillance from the beginning, largely to track the success of the program and further our understanding of the epidemiology of the disease. Early observations in West Africa, bolstered by later data from Indonesia and the Asian subcontinent, showed that smallpox did not spread rapidly, and outbreaks could be quickly controlled by isolation of patients and vaccination of their contacts. Contacts were usually easy to find because transmission of smallpox usually required prolonged face-to-face contact. The emphasis therefore shifted to active searches to find cases, coupled with contact tracing, rigorous isolation of patients, and vaccination and surveillance of contacts to contain outbreaks. This shift away from mass vaccination resulted in an acceleration of the program's success.